Run RADproc

Runs RADproc. The approach replaces ustacks and cstacks steps. Read the paper for more information. Read stackr vignette.

run_radproc(
  file.type = "gzfastq",
  f = "04_process_radtags",
  o = "06_ustacks_2_gstacks",
  a = FALSE,
  M = 2,
  m = 3,
  n = 2,
  parallel.core = parallel::detectCores() - 1,
  x = 3,
  S = 2,
  D = 7,
  cmd.path = "/usr/local/bin/RADProc"
)

Arguments

file.type

(character) Input file Type. Supported types: fasta, fastq, gzfasta, or gzfastq. Default: file.type = "gzfastq".

f

(path) Input file path. Usually, the stacks process_radtags output folder. Default: f = "04_process_radtags".

o

(path) Output path to write results. Default: o = "06_ustacks_2_gstacks".

a

(logical) Enable parameter sweep mode. Default: a = FALSE. Please use run_ustacks with mismatch testing.

M

Maximum distance (in nucleotides) allowed between stacks to form network. Default: M = 2.

m

Minimum depth of coverage. Default: m = 3.

n

Maximum distance (in nucleotides) allowed between catalog loci to merge Default: n = 2.

parallel.core

(integer) Enable parallel execution with num_threads threads. Default: parallel.core = parallel::detectCores() - 1.

x

(integer) Maximum number stacks per locus. Default: x = 3.

S

(percentage) Minimum sample percentage. Default: S = 30.

D

(percentage) Minimum average coverage depth. Default: D = 7.

cmd.path

(character, path) Provide the FULL path to RADProc program. See details on how to install RADProc in stackr vignette. Default: cmd.path = "/usr/local/bin/RADProc".

Value

Returns 3 files per samples: .snps.tsv, .tags.tsv, .alleles.tsv. Also returns 3 catalog files: catalog.snps.tsv, catalog.tags.tsv, catalog.alleles.tsv.

References

Ravindran, P., Bentzen, P., Bradbury, I., Beiko, R. (2019). RADProc: A computationally efficient de novo locus assembler for population studies using RADseq data. Molecular Ecology Resources 19(1), 272-282. https://dx.doi.org/10.1111/1755-0998.12954

See also

RADproc.

Examples

if (FALSE) { # \dontrun{
# The simplest form of the function:
u <- stackr::run_radproc() # that's it !
} # }